This update of RNAiDB includes all RNAi data from the Piano lab, and all RNAi experiments in WormBase WS150. Reagent to gene mappings are curated at RNAiDB and may differ from those available at WormBase (explain ...).

RNAiDB v5.0 features:

Website redesign: the website infrastructure has been completely overhauled and the interface redesigned to improve the user interface and maintainability. Changes to all pages and gene graphs have been implemented.

Integration with WormBase WS150: RNAiDB v5 incorporates all RNAi experiments present in WS150, including annotated phenotypes and raw data (images and time-lapse movies). Reagent to gene mappings are annotated independently at RNAiDB using a sliding n-mer window method to evaluate sequence similarity between dsRNA reagents and predicted transcripts. Primary (canonical) and secondary (off-target) RNAi targets identified in this way may differ from targets identified at WormBase using BLAST/BLAT.

Sliding window analysis: calculation of potential off-target inhibition has been reimplemented to streamline the analysis with generation of GFF annotations.

Search by chromosomal location or interval has been added, which allows the discovery of all RNAi results within a specified interval on the physical map. This can help users identify potential candidate genes for genetic mutations mapped to a rough physical interval.

Links to N-Browse: N-Browse is a web-based interactive graphical browser for molecular interaction data developed by Huey-Ling Kao in the Gunsalus lab. N-Browse allows the integrated analysis of heterogeneous functiona links between genes and proteins, such as protein-protein and genetic interactions, co-expression, phenotypic correlations, and predicted miRNA-target interactions. N-Browse can be used to visualize data in
Gunsalus et al., 2005)
and is described briefly in
Lall et al., 2006.

This study reports the identification and phenotypic characterization of 661 genes with phenotypes in the early embryo (up to the 2-cell stage) in an RNAi survey of over 95% of C. elegans genes. In RNAiDB, experiment names from this study begin with "Cenix:". A phenotypic signature of 45 characters was generated for each of the 661 genes. The 661 Cenix Early Embryonic phenotypic signatures can now be queried using PhenoBlast.

In this study RNAi was performed using ORFeome clones for over 1,000 genes with transcripts enriched in the ovary with no previously identified embryonic phenotypes. 155 new genes with roles in embryogenesis were identified, raising the total number of known embryonic essential genes to ~1,800. Notably, over two-thirds of the newly identified genes showed partial penetrance lethality, suggesting that most genes with strong embryonic phenotypes have already been identified. Experiment names from this study begin with "PF:ORC_" in RNAiDB.

This study reports the first large-scale RNAi screen in C. elegans. Clones from an ovary cDNA library were screened for embryonic lethality and 81 genes with phenotypes in the early embryo were analyzed and grouped into phenotypic classes. Experiment names from this study begin with "KK:SP" in RNAiDB.